Spectronaut™ 13


Spectronaut is the most advanced software for DIA proteomics, providing more identifications with a higher level of confidence. Thanks to the embedded search engine Pulsar, it enables complete workflows from library generation to data analysis. With its latest release, Spectronaut establishes novel solutions to current challenges in the field of proteomics.



DIA, with its high reproducibility, is inherently well suited for PTM analysis. With a new site localization confidence algorithm, Spectronaut is now fully enabled for robust, sensitive, and reliable PTM quantification.



Innovative acquisition methods like BoxCar, available on new Thermo Scientific instruments can increase the MS1 dynamic range by more than one order of magnitude (Meier et al., 2018). This is particularly valuable for samples that are challenging like plasma, urine, and cerebrospinal fluid (CSF). Spectronaut gives access to the benefits of BoxCar in combination with DIA in its most recent release.


We have many more new features! Some of them are:

  • Deep learning assisted iRT calibration for library generation: Generate an empirical library with high precision iRT calibration even if your organism is an uncommon one.

  • Highly improved memory management: Improved scalability for very large experiments (10,000s of runs). Spectronaut is even faster now!

  • Implementation of quantification imputing strategies: Improved quantification strategies for missing values.



«Spectronaut’s novel PTM localization algorithm puts a powerful tool in our hands, providing exciting new possibilities in phosphoproteomics research.»

Prof. Dr. Jesper Velgaard Olsen,
CPR University of Copenhagen


Post-translational modification (PTM) studies are key to understanding important aspects of protein function. Now the accuracy and sensitivity of DIA can be combined with a powerful algorithm for site localization implemented in Spectronaut for a robust, sensitive, and reliable PTM analysis.



PTM studies have traditionally been performed using data-dependent acquisition (DDA). However, data-independent acquisition (DIA) could provide a better alternative with higher proteome coverage, quantification accuracy, and sensitivity. To test the quantification precision and accuracy of DIA in a realistic PTM study context, yeast proteome was spiked into a complex HeLa background and this mixture was phospho-enriched. The DIA data showed higher quantitative precision and accuracy as compared to DDA (top figure).

The advantages of DIA compared to DDA are even more significant in PTM studies. Two of the main advantages of DIA for PTM discovery are 1) no MS2 information is lost, avoiding the risk of missing your precursor during fragmentation; 2) the extra RT dimension for MS2 information increases the localization confidence. To assess these advantages, synthetic phosphopeptides were spiked in a yeast phosphopeptide background in different concentrations. In the bottom figure, we show the performance of DIA and Spectronaut compared to DDA when assigning localization for PTMs. DIA and Spectronaut perform particularly well for low abundant phosphopeptides.

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